Publications

@article{info:hdl:2013/343811,

title = {GNN-based embedding for clustering scRNA-seq data},

author = {Madalina Ciortan and Matthieu Defrance},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/343811},

year  = {2022},

date = {2022-01-01},

journal = {Bioinformatics},

volume = {38},

number = {4},

pages = {1037-1044},

note = {DOI: 10.1093/bioinformatics/btab787},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/339040,

title = {Voluntary safety commitments provide an escape from over-regulation in AI development},

author = {The Anh T. A. H. Han and Tom Lenaerts and Francisco C. Santos and Luís Moniz Pereira},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/339040},

year  = {2022},

date = {2022-01-01},

journal = {Technology in society},

volume = {68},

note = {DOI: 10.1016/j.techsoc.2021.101843},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/342471,

title = {A Digital Twin Approach for Improving Estimation Accuracy in Dynamic Thermal Rating of Transmission Lines},

author = {Gian Marco Paldino and Fabrizio De Caro and Jacopo De Stefani and Alfredo A. Vaccaro and Domenico D. Villacci and Gianluca Bontempi},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/342471},

year  = {2022},

date = {2022-01-01},

journal = {Energies},

volume = {15},

number = {6},

note = {DOI: 10.3390/en15062254},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/342417,

title = {Scaling up oligogenic diseases research with OLIDA: The Oligogenic Diseases Database},

author = {Charlotte Nachtegael and Barbara Gravel and Arnau Dillen and Guillaume Smits and Ann Nowe and Sofia Papadimitriou and Tom Lenaerts},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/342417},

year  = {2022},

date = {2022-01-01},

journal = {Database},

volume = {2022},

note = {DOI: 10.1093/database/baac023},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/344327,

title = {Inferring strategies from observations in long iterated Prisoner’s dilemma experiments},

author = {Eladio Montero-Porras and Jelena Grujić and Elias Fernández Domingos and Tom Lenaerts},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/344327},

year  = {2022},

date = {2022-01-01},

journal = {Scientific reports},

volume = {12},

number = {1},

note = {DOI: 10.1038/s41598-022-11654-2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/341515,

title = {Artificial intelligence development races in heterogeneous settings},

author = {Theodor Cimpeanu and Francisco C. Santos and Luís Marcelo Pereira and Tom Lenaerts and The Anh T. A. H. Han},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/341515},

year  = {2022},

date = {2022-01-01},

journal = {Scientific reports},

volume = {12},

number = {1},

note = {DOI: 10.1038/s41598-022-05729-3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/335472,

title = {Information criteria bias correction for group selection},

author = {Bastien Marquis and Maarten Jansen},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/335472},

year  = {2022},

date = {2022-01-01},

journal = {Statistical papers},

note = {Language of publication: fr},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/335292,

title = {Predicting Reach to Find Persuadable Customers: Improving Uplift Models for Churn Prevention},

author = {Theo Verhelst and Jeevan Shrestha and Denis Mercier and Jean Christophe Dewitte and Gianluca Bontempi},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/335292},

year  = {2021},

date = {2021-01-01},

journal = {Lecture notes in computer science},

volume = {12986 LNAI},

pages = {44-54},

note = {DOI: 10.1007/978-3-030-88942-5_4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/326786,

title = {AST-MTL: An Attention-based Multi-Task Learning Strategy for Traffic Forecasting},

author = {Giovanni Buroni and Bertrand Lebichot and Gianluca Bontempi},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/326786},

year  = {2021},

date = {2021-01-01},

journal = {IEEE access},

note = {DOI: 10.1109/ACCESS.2021.3083412},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/320376,

title = {Mediating artificial intelligence developments through negative and positive incentives},

author = {The Anh T. A. H. Han and Luís Moniz Pereira and Tom Lenaerts and Francisco F. C. Santos},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/320376},

year  = {2021},

date = {2021-01-01},

journal = {PloS one},

volume = {16},

number = {1 January},

note = {DOI: 10.1371/journal.pone.0244592},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/321049b,

title = {Repeated interaction and its impact on cooperation and surplus allocation—an experimental analysis},

author = {Sibilla Di Guida and The Anh T. A. H. Han and Georg Kirchsteiger and Tom Lenaerts and Ioannis Zisis},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/321049},

year  = {2021},

date = {2021-01-01},

journal = {Games},

volume = {12},

number = {1},

note = {DOI: 10.3390/g12010025},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/316657,

title = {NR5A1 c.991-1G > C splice-site variant causes familial 46,XY partial gonadal dysgenesis with incomplete penetrance},

author = {Maris Laan and Laura Kasak and Kęstutis Timinskas and Marina Grigorova and Česlovas Venclovas and Alexandre Renaux and Tom Lenaerts and Margus Punab},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/316657},

year  = {2021},

date = {2021-01-01},

journal = {Clinical endocrinology},

note = {DOI: 10.1111/cen.14381},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/322462b,

title = {Multistage feedback-driven compartmental dynamics of hematopoiesis},

author = {Nathaniel Vincent Mon P`ere and Tom Lenaerts and Jorge Manuel dos Santos J. M. d. S. Pacheco and David Dingli},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/322462},

year  = {2021},

date = {2021-01-01},

journal = {iScience},

volume = {24},

number = {4},

note = {DOI: 10.1016/j.isci.2021.102326},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/332290,

title = {Molecular adaptations to heat stress in the thermophilic ant genus Cataglyphis},

author = {Rémy Perez and Natalia Souza Araujo and Matthieu Defrance and Serge Aron},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/332290},

year  = {2021},

date = {2021-01-01},

journal = {Molecular ecology},

note = {DOI: 10.1111/mec.16134},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/325214b,

title = {Contrastive self-supervised clustering of scRNA-seq data.},

author = {Madalina Ciortan and Matthieu Defrance},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/325214},

year  = {2021},

date = {2021-01-01},

journal = {BMC bioinformatics},

volume = {22},

number = {1},

pages = {280},

note = {DOI: 10.1186/s12859-021-04210-8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/330754,

title = {Modeling behavioral experiments on uncertainty and cooperation with population-based reinforcement learning},

author = {Elias Fernández Domingos and Jelena Grujić and Juan Carlos Burguillo and Francisco C. Santos and Tom Lenaerts},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/330754},

year  = {2021},

date = {2021-01-01},

journal = {Simulation modelling practice and theory},

volume = {109},

note = {DOI: 10.1016/j.simpat.2021.102299},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/322517b,

title = {A tutorial on network-wide multi-horizon traffic forecasting with deep learning},

author = {Giovanni Buroni and Gianluca Bontempi and Karl Determe},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/322517},

year  = {2021},

date = {2021-01-01},

journal = {CEUR Workshop Proceedings},

volume = {2841},

note = {Language of publication: en},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/321123b,

title = {The CLAIRE COVID-19 initiative: approach, experiences and recommendations},

author = {Gianluca Bontempi and Ricardo Chavarriaga and Hans Canck and Emanuela Girardi and Holger H. Hoos and Iarla Kilbane-Dawe and Tonio Ball and Ann Nowe and Jose Sousa and Davide Bacciu and Marco Aldinucci and Manlio Domenico and Alessandro Saffiotti and Marco Maratea},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/321123},

year  = {2021},

date = {2021-01-01},

journal = {Ethics and information technology},

note = {DOI: 10.1007/s10676-020-09567-7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/331459,

title = {A Modern Reconstruction of Richard Carrington’s Observations (1853–1861)},

author = {S. Bhattacharya and E. T. H. Teague and Susanne Fay and Laure Lef`evre and Maarten Jansen and Frédéric L. Clette},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/331459},

year  = {2021},

date = {2021-01-01},

journal = {Solar physics},

volume = {296},

number = {8},

note = {DOI: 10.1007/s11207-021-01864-8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/331774,

title = {Incremental learning strategies for credit cards fraud detection},

author = {Bertrand Lebichot and Gian Marco Paldino and Wissam Siblini and Liyun He-Guelton and Frédéric Oblé and Gianluca Bontempi},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/331774},

year  = {2021},

date = {2021-01-01},

journal = {International journal of data science and analytics (Print)},

volume = {12},

number = {2},

pages = {165-174},

note = {DOI: 10.1007/s41060-021-00258-0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/333678,

title = {DNAModAnnot: A R toolbox for DNA modification filtering and annotation},

author = {Alexis Hardy and Mélody Matelot and Amandine Touzeau and Christophe Klopp and Céline Lopez-Roques and Sandra Duharcourt and Matthieu Defrance},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/333678},

year  = {2021},

date = {2021-01-01},

journal = {Bioinformatics},

volume = {37},

number = {17},

pages = {2738-2740},

note = {DOI: 10.1093/bioinformatics/btab032},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/331622,

title = {Transfer Learning Strategies for Credit Card Fraud Detection},

author = {Bertrand Lebichot and Theo Verhelst and Yann-A"el Le Borgne and Liyun He-Guelton and Frédéric Oblé and Gianluca Bontempi},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/331622},

year  = {2021},

date = {2021-01-01},

journal = {IEEE access},

volume = {9},

pages = {114754-114766},

note = {DOI: 10.1109/ACCESS.2021.3104472},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/332056,

title = {Factor-Based Framework for Multivariate and Multi-step-ahead Forecasting of Large Scale Time Series},

author = {Jacopo De Stefani and Gianluca Bontempi},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/332056},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in Big Data},

volume = {4},

note = {DOI: 10.3389/fdata.2021.690267},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/334299,

title = {TIGER: The gene expression regulatory variation landscape of human pancreatic islets.},

author = {Lorena Alonso and Anthony Piron and Ignasi Morán and Marta Guindo-Martínez and Sílvia Bon`as-Guarch and Goutham Atla and Irene Miguel-Escalada and Romina Royo and Montserrat Puiggr`os and Xavier Garcia-Hurtado and Mara Suleiman and Lorella Marselli and Jonathan L S Esguerra and Jean Valéry Turatsinze and Jason M Torres and Vibe Nylander and Ji Chen and Lena Eliasson and Matthieu Defrance and Ramon Amela and MAGIC and Hindrik Mulder and Anna L Gloyn and Leif Groop and Piero Marchetti and Decio L. Eizirik and Jorge Ferrer and Josep JM Mercader and Miriam Cnop and David Torrents},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/334299},

year  = {2021},

date = {2021-01-01},

journal = {Cell reports},

volume = {37},

number = {2},

pages = {109807},

note = {DOI: 10.1016/j.celrep.2021.109807},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/331277,

title = {DOME: recommendations for supervised machine learning validation in biology},

author = {Ian Walsh and Dmytro Fishman and Dario Garcia-Gasulla and Tiina Titma and Gianluca Pollastri and Emidio Capriotti and Rita RC Casadio and Salvador Capella-Gutierrez and Davide Cirillo and Alessio Del Conte and Alexandros A. C. Dimopoulos and Victoria Dominguez Del Angel and Joaquin Dopazo and Piero Fariselli and José Maria Fernández and Florian Huber and Anna Kreshuk and Tom Lenaerts and Pier Luigi Martelli and Arcadi Navarro and Pilib Broin and Janet Pi nero and Damiano Piovesan and Martin Reczko and Francesco Ronzano and Venkata Satagopam and Castrense Savojardo and Vojtěch Spiwok and Marco Antonio Tangaro and Giacomo Tartari and David Salgado and Alfonso Valencia and Federico Zambelli and Jennifer Harrow and Fotis F. E. Psomopoulos and Silvio S. C. E. Tosatto},

url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/331277},

year  = {2021},

date = {2021-01-01},

journal = {Nature methods},

note = {DOI: 10.1038/s41592-021-01205-4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/322517,

title = {A tutorial on network-wide multi-horizon traffic forecasting with deep learning},

author = {Giovanni Buroni and Gianluca Bontempi and Karl Determe},

url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/322517/3/EasyChair-Preprint-4944.pdf},

year  = {2021},

date = {2021-01-01},

journal = {CEUR Workshop Proceedings},

volume = {2841},

abstract = {Traffic flow forecasting is fundamental to today's Intelligent Transportation Systems (ITS). It involves the task of learning traffic complex dynamics in order to predict future conditions. This is particularly challenging when it comes to predict the traffic status for multiple horizons into the future and at the same time for the entire transportation network. In this context deep learning models have recently shown promising results. This models can inherently capture the non-linear space-temporal correlations (ST) in traffic by taking advantage of the huge volume of data available. In this study the authors present a LSTM encoder-decoder for multi-horizon traffic flow predictions. We adopted a direct approach in which the model simultaneously predict traffic conditions for the entire Belgian motorway transport network at each time step. The results clearly show the superiority of this model when compared with other deep learning models. In the workshop, conference attendees will learn how to process and visualize mobility data, obtain optimal features for traffic flow forecasting, build a LSTM encoder-decoder and perform predictions in an online manner.},

note = {Language of publication: en},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/321123,

title = {The CLAIRE COVID-19 initiative: approach, experiences and recommendations},

author = {Gianluca Bontempi and Ricardo Chavarriaga and Hans eD Canck and Emanuela Girardi and Holger H Hoos and Iarla Kilbane-Dawe and Tonio Ball and Ann Nowe and Jose Sousa and Davide Bacciu and Marco Aldinucci and Manlio eD Domenico and Alessandro Saffiotti and Marco Maratea},

url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/321123/3/Bontempi2021_Article_TheCLAIRECOVID-19InitiativeApp-2.pdf},

year  = {2021},

date = {2021-01-01},

journal = {Ethics and information technology},

abstract = {A volunteer effort by Artificial Intelligence (AI) researchers has shown it can deliver significant research outcomes rapidly to help tackle COVID-19. Within two months, CLAIRE's self-organising volunteers delivered the World's first comprehensive curated repository of COVID-19-related datasets useful for drug-repurposing, drafted review papers on the role CT/X-ray scan analysis and robotics could play, and progressed research in other areas. Given the pace required and nature of voluntary efforts, the teams faced a number of challenges. These offer insights in how better to prepare for future volunteer scientific efforts and large scale, data-dependent AI collaborations in general. We offer seven recommendations on how to best leverage such efforts and collaborations in the context of managing future crises.},

note = {DOI: 10.1007/s10676-020-09567-7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/321049,

title = {Repeated interaction and its impact on cooperation and surplus allocation---an experimental analysis},

author = {Sibilla Di Guida and The Anh T A H Han and Georg Kirchsteiger and Tom Lenaerts and Ioannis Zisis},

url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/321049/1/doi_304693.pdf},

year  = {2021},

date = {2021-01-01},

journal = {Games},

volume = {12},

number = {1},

abstract = {This paper investigates how the possibility of affecting group composition combined with the possibility of repeated interaction impacts cooperation within groups and surplus distribution. We developed and tested experimentally a Surplus Allocation Game where cooperation of four agents is needed to produce surplus, but only two have the power to allocate it among the group members. Three matching procedures (corresponding to three separate experimental treatments) were used to test the impact of the variables of interest. A total of 400 subjects participated in our research, which was computer-based and conducted in a laboratory. Our results show that allowing for repeated interaction with the same partners leads to a self-selection of agents into groups with different life spans, whose duration is correlated with the behavior of both distributors and receivers. While behavior at the group level is diverse for surplus allocation and amount of cooperation, aggregate behavior is instead similar when repeated interaction is allowed or not allowed. We developed a behavioral model that captures the dynamics observed in the experimental data and sheds light into the rationales that drive the agents' individual behavior, suggesting that the most generous distributors are those acting for fear of rejection, not for true generosity, while the groups lasting the longest are those composed by this type of distributors and ``undemanding'' receivers.},

note = {DOI: 10.3390/g12010025},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/322462,

title = {Multistage feedback-driven compartmental dynamics of hematopoiesis},

author = {Nathaniel Vincent Mon P{`e}re and Tom Lenaerts and Jorge Manuel Santos J M d S dos Pacheco and David Dingli},

url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/322462/1/doi_306106.pdf},

year  = {2021},

date = {2021-01-01},

journal = {iScience},

volume = {24},

number = {4},

abstract = {Human hematopoiesis is surprisingly resilient to disruptions, providing suitable responses to severe bleeding, long-lasting immune activation, and even bone marrow transplants. Still, many blood disorders exist which push the system past its natural plasticity, resulting in abnormalities in the circulating blood. While proper treatment of such diseases can benefit from understanding the underlying cell dynamics, these are non-trivial to predict due to the hematopoietic system's hierarchical nature and complex feedback networks. To characterize the dynamics following different types of perturbations, we investigate a model representing hematopoiesis as a sequence of compartments covering all maturation stages---from stem to mature cells---where feedback regulates cell production to ongoing necessities. We find that a stable response to perturbations requires the simultaneous adaptation of cell differentiation and self-renewal rates, and show that under conditions of continuous disruption---as found in chronic hemolytic states---compartment cell numbers evolve to novel stable states.},

note = {DOI: 10.1016/j.isci.2021.102326},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/322914,

title = {Mg deficiency interacts with the circadian clock and phytochromes pathways in Arabidopsis},

author = {Quentin Rivi{`e}re and Qiying Xiao and Annelie Gutsch and Matthieu Defrance and A A R Webb and Nathalie Verbruggen},

url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/322914/3/MgDeficiencyInPlantsLightClock.pdf},

year  = {2021},

date = {2021-01-01},

journal = {Annals of Applied Biology},

volume = {178},

number = {2},

pages = {387-399},

note = {DOI: 10.1111/aab.12659},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{info:hdl:2013/325214,

title = {Contrastive self-supervised clustering of scRNA-seq data.},

author = {Madalina Ciortan and Matthieu Defrance},

url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/325214/1/doi_308858.pdf},

year  = {2021},

date = {2021-01-01},

journal = {BMC bioinformatics},

volume = {22},

number = {1},

pages = {280},

abstract = {Single-cell RNA sequencing (scRNA-seq) has emerged has a main strategy to study transcriptional activity at the cellular level. Clustering analysis is routinely performed on scRNA-seq data to explore, recognize or discover underlying cell identities. The high dimensionality of scRNA-seq data and its significant sparsity accentuated by frequent dropout events, introducing false zero count observations, make the clustering analysis computationally challenging. Even though multiple scRNA-seq clustering techniques have been proposed, there is no consensus on the best performing approach. On a parallel research track, self-supervised contrastive learning recently achieved state-of-the-art results on images clustering and, subsequently, image classification.},

note = {DOI: 10.1186/s12859-021-04210-8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}